Jimmy Neutron was originally created in the 1980s by Keith Alcorn and John A. Davis under the name Johnny Quasar, in a script titled Runaway Rocketboy that was ultimately abandoned.

Davis later reworked the idea as a short film called Johnny Quasar, which he presented at SIGGRAPH, where he met Steve Oedekerk and began developing both a TV series and a movie based on it.

The character's name was changed from Johnny Quasar to Jimmy Neutron because it was thought to sound too similar to Jonny Quest.

An early pilot episode was originally meant to air as a short on the show KaBlam!, but that program was canceled before the episode could air.

The pilot featured several differences from the final series, including Jimmy wearing a red and white striped shirt instead of his iconic red atom shirt, a different design for Carl Wheezer, and the absence of characters Sheen Estevez, Cindy Vortex, and Libby Folfax.

The show's theme song was originally written and recorded by Brian Causey of the band Man or Astro-man? for the pilot episode, and this original version was ultimately kept for the TV series rather than the extended version later made by Bowling for Soup for the film.

DNA Productions developed special custom code allowing animators to animate scenes in Maya that could then be rendered in Lightwave, helping the team meet deadlines and stay within budget when transitioning from the film to the TV series.

In 2016, creator John A. Davis revealed he had a story ready for a Jimmy Neutron reboot feature film but was waiting for the right situation to make it, and in 2025 screenwriter Adam Pava confirmed a new film project had been in development since December 2023.